Starting phenix.real_space_refine on Mon Aug 5 09:12:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u5h_41922/08_2024/8u5h_41922.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u5h_41922/08_2024/8u5h_41922.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u5h_41922/08_2024/8u5h_41922.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u5h_41922/08_2024/8u5h_41922.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u5h_41922/08_2024/8u5h_41922.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u5h_41922/08_2024/8u5h_41922.cif" } resolution = 3.23 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 2.051 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 314 5.49 5 S 15 5.16 5 C 7463 2.51 5 N 2514 2.21 5 O 3130 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "J GLU 52": "OE1" <-> "OE2" Residue "K GLU 92": "OE1" <-> "OE2" Residue "O GLU 59": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 13436 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 281 Classifications: {'peptide': 41} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 3, 'TRANS': 37} Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 95 Unresolved non-hydrogen dihedrals: 69 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 3, 'TRP:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 47 Chain: "B" Number of atoms: 163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 163 Classifications: {'peptide': 23} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 2, 'TRANS': 20} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "C" Number of atoms: 3200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 3200 Classifications: {'DNA': 157} Link IDs: {'rna3p': 156} Chain: "D" Number of atoms: 488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 488 Classifications: {'peptide': 66} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 3, 'TRANS': 62} Chain breaks: 2 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 31 Chain: "H" Number of atoms: 3237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 3237 Classifications: {'DNA': 157} Link IDs: {'rna3p': 156} Chain: "I" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 807 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 94} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "J" Number of atoms: 676 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 84, 667 Classifications: {'peptide': 84} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 82} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Conformer: "B" Number of residues, atoms: 84, 667 Classifications: {'peptide': 84} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 82} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 664 Chain: "K" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 824 Classifications: {'peptide': 110} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 104} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 10 Chain: "M" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 731 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 92} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "O" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 816 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 94} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "Q" Number of atoms: 647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 647 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 81} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "R" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 825 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 102} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "S" Number of atoms: 741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 741 Classifications: {'peptide': 96} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 93} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ALYS J 20 " occ=0.77 ... (16 atoms not shown) pdb=" NZ BLYS J 20 " occ=0.23 Time building chain proxies: 7.66, per 1000 atoms: 0.57 Number of scatterers: 13436 At special positions: 0 Unit cell: (90.1331, 127.174, 122.235, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 15 16.00 P 314 15.00 O 3130 8.00 N 2514 7.00 C 7463 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.05 Conformation dependent library (CDL) restraints added in 1.5 seconds 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1694 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 10 sheets defined 64.7% alpha, 4.1% beta 153 base pairs and 259 stacking pairs defined. Time for finding SS restraints: 6.51 Creating SS restraints... Processing helix chain 'A' and resid 199 through 210 Processing helix chain 'B' and resid 173 through 177 removed outlier: 3.589A pdb=" N GLU B 177 " --> pdb=" O LEU B 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 35 removed outlier: 3.606A pdb=" N ILE D 30 " --> pdb=" O VAL D 26 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLN D 31 " --> pdb=" O LYS D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 39 No H-bonds generated for 'chain 'D' and resid 37 through 39' Processing helix chain 'D' and resid 56 through 60 Processing helix chain 'I' and resid 44 through 57 removed outlier: 4.226A pdb=" N LEU I 48 " --> pdb=" O GLY I 44 " (cutoff:3.500A) Processing helix chain 'I' and resid 63 through 79 removed outlier: 3.854A pdb=" N ASP I 77 " --> pdb=" O GLU I 73 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N PHE I 78 " --> pdb=" O ILE I 74 " (cutoff:3.500A) Processing helix chain 'I' and resid 85 through 114 removed outlier: 3.638A pdb=" N MET I 90 " --> pdb=" O ARG I 86 " (cutoff:3.500A) Processing helix chain 'I' and resid 120 through 131 Processing helix chain 'J' and resid 25 through 29 Processing helix chain 'J' and resid 30 through 42 Processing helix chain 'J' and resid 49 through 76 removed outlier: 4.043A pdb=" N GLU J 53 " --> pdb=" O LEU J 49 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ARG J 55 " --> pdb=" O TYR J 51 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASP J 68 " --> pdb=" O ASN J 64 " (cutoff:3.500A) Processing helix chain 'J' and resid 82 through 94 Processing helix chain 'K' and resid 16 through 22 Processing helix chain 'K' and resid 26 through 37 Processing helix chain 'K' and resid 45 through 73 removed outlier: 4.247A pdb=" N VAL K 49 " --> pdb=" O ALA K 45 " (cutoff:3.500A) Processing helix chain 'K' and resid 79 through 88 removed outlier: 3.722A pdb=" N LEU K 83 " --> pdb=" O ILE K 79 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLN K 84 " --> pdb=" O PRO K 80 " (cutoff:3.500A) Processing helix chain 'K' and resid 90 through 97 Processing helix chain 'M' and resid 34 through 46 Processing helix chain 'M' and resid 52 through 81 removed outlier: 3.853A pdb=" N ASN M 81 " --> pdb=" O LEU M 77 " (cutoff:3.500A) Processing helix chain 'M' and resid 87 through 99 Processing helix chain 'M' and resid 101 through 119 removed outlier: 3.887A pdb=" N SER M 109 " --> pdb=" O LYS M 105 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N TYR M 118 " --> pdb=" O ALA M 114 " (cutoff:3.500A) Processing helix chain 'O' and resid 45 through 57 removed outlier: 3.577A pdb=" N ARG O 49 " --> pdb=" O THR O 45 " (cutoff:3.500A) Processing helix chain 'O' and resid 63 through 76 Processing helix chain 'O' and resid 85 through 114 Processing helix chain 'O' and resid 120 through 132 removed outlier: 3.507A pdb=" N ILE O 124 " --> pdb=" O MET O 120 " (cutoff:3.500A) Processing helix chain 'Q' and resid 25 through 29 removed outlier: 3.507A pdb=" N ILE Q 29 " --> pdb=" O ILE Q 26 " (cutoff:3.500A) Processing helix chain 'Q' and resid 30 through 42 Processing helix chain 'Q' and resid 49 through 76 removed outlier: 3.580A pdb=" N GLU Q 53 " --> pdb=" O LEU Q 49 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N ARG Q 55 " --> pdb=" O TYR Q 51 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ASP Q 68 " --> pdb=" O ASN Q 64 " (cutoff:3.500A) Processing helix chain 'Q' and resid 82 through 93 Processing helix chain 'R' and resid 16 through 22 Processing helix chain 'R' and resid 26 through 37 Processing helix chain 'R' and resid 45 through 73 removed outlier: 4.346A pdb=" N VAL R 49 " --> pdb=" O ALA R 45 " (cutoff:3.500A) Processing helix chain 'R' and resid 79 through 89 Processing helix chain 'R' and resid 90 through 97 Processing helix chain 'S' and resid 34 through 46 Processing helix chain 'S' and resid 52 through 81 removed outlier: 4.154A pdb=" N ASN S 81 " --> pdb=" O LEU S 77 " (cutoff:3.500A) Processing helix chain 'S' and resid 87 through 99 Processing helix chain 'S' and resid 101 through 121 removed outlier: 3.578A pdb=" N LYS S 105 " --> pdb=" O GLY S 101 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 13 through 16 removed outlier: 3.759A pdb=" N LEU D 15 " --> pdb=" O ILE D 3 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'I' and resid 83 through 84 removed outlier: 6.851A pdb=" N ARG I 83 " --> pdb=" O VAL J 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'I' and resid 118 through 119 Processing sheet with id=AA4, first strand: chain 'J' and resid 96 through 98 removed outlier: 6.848A pdb=" N THR J 96 " --> pdb=" O THR R 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'K' and resid 42 through 43 removed outlier: 7.109A pdb=" N ARG K 42 " --> pdb=" O ILE M 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'K' and resid 77 through 78 Processing sheet with id=AA7, first strand: chain 'K' and resid 100 through 102 Processing sheet with id=AA8, first strand: chain 'O' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'R' and resid 42 through 43 removed outlier: 7.880A pdb=" N ARG R 42 " --> pdb=" O ILE S 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'R' and resid 77 through 78 424 hydrogen bonds defined for protein. 1251 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 385 hydrogen bonds 750 hydrogen bond angles 0 basepair planarities 153 basepair parallelities 259 stacking parallelities Total time for adding SS restraints: 5.09 Time building geometry restraints manager: 7.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2494 1.33 - 1.45: 4642 1.45 - 1.57: 6525 1.57 - 1.69: 626 1.69 - 1.81: 26 Bond restraints: 14313 Sorted by residual: bond pdb=" P DC H 48 " pdb=" OP2 DC H 48 " ideal model delta sigma weight residual 1.480 1.521 -0.041 2.00e-02 2.50e+03 4.13e+00 bond pdb=" P DT C 214 " pdb=" OP2 DT C 214 " ideal model delta sigma weight residual 1.480 1.520 -0.040 2.00e-02 2.50e+03 4.00e+00 bond pdb=" P DA C 220 " pdb=" OP2 DA C 220 " ideal model delta sigma weight residual 1.480 1.519 -0.039 2.00e-02 2.50e+03 3.82e+00 bond pdb=" P DC H 114 " pdb=" OP2 DC H 114 " ideal model delta sigma weight residual 1.480 1.519 -0.039 2.00e-02 2.50e+03 3.80e+00 bond pdb=" P DT C 170 " pdb=" OP2 DT C 170 " ideal model delta sigma weight residual 1.480 1.518 -0.038 2.00e-02 2.50e+03 3.67e+00 ... (remaining 14308 not shown) Histogram of bond angle deviations from ideal: 97.62 - 104.88: 1263 104.88 - 112.14: 7977 112.14 - 119.40: 4372 119.40 - 126.65: 6150 126.65 - 133.91: 937 Bond angle restraints: 20699 Sorted by residual: angle pdb=" O3' DT C 214 " pdb=" P DC C 215 " pdb=" O5' DC C 215 " ideal model delta sigma weight residual 104.00 99.13 4.87 1.50e+00 4.44e-01 1.05e+01 angle pdb=" C3' DG H 135 " pdb=" O3' DG H 135 " pdb=" P DG H 136 " ideal model delta sigma weight residual 120.20 124.81 -4.61 1.50e+00 4.44e-01 9.44e+00 angle pdb=" C GLY K 37 " pdb=" N ASN K 38 " pdb=" CA ASN K 38 " ideal model delta sigma weight residual 121.54 127.40 -5.86 1.91e+00 2.74e-01 9.41e+00 angle pdb=" O3' DT H 49 " pdb=" P DT H 50 " pdb=" O5' DT H 50 " ideal model delta sigma weight residual 104.00 99.49 4.51 1.50e+00 4.44e-01 9.05e+00 angle pdb=" O3' DG C 205 " pdb=" P DT C 206 " pdb=" O5' DT C 206 " ideal model delta sigma weight residual 104.00 99.77 4.23 1.50e+00 4.44e-01 7.94e+00 ... (remaining 20694 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.81: 6275 35.81 - 71.62: 1468 71.62 - 107.43: 29 107.43 - 143.24: 6 143.24 - 179.05: 21 Dihedral angle restraints: 7799 sinusoidal: 5181 harmonic: 2618 Sorted by residual: dihedral pdb=" C4' DA H 5 " pdb=" C3' DA H 5 " pdb=" O3' DA H 5 " pdb=" P DT H 6 " ideal model delta sinusoidal sigma weight residual 220.00 40.95 179.05 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DC C 224 " pdb=" C3' DC C 224 " pdb=" O3' DC C 224 " pdb=" P DT C 225 " ideal model delta sinusoidal sigma weight residual -140.00 37.49 -177.49 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DA C 309 " pdb=" C3' DA C 309 " pdb=" O3' DA C 309 " pdb=" P DT C 310 " ideal model delta sinusoidal sigma weight residual -140.00 34.44 -174.44 1 3.50e+01 8.16e-04 1.56e+01 ... (remaining 7796 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.122: 2337 0.122 - 0.243: 11 0.243 - 0.365: 0 0.365 - 0.486: 0 0.486 - 0.608: 19 Chirality restraints: 2367 Sorted by residual: chirality pdb=" P DG H 136 " pdb=" OP1 DG H 136 " pdb=" OP2 DG H 136 " pdb=" O5' DG H 136 " both_signs ideal model delta sigma weight residual True 2.35 -2.95 -0.61 2.00e-01 2.50e+01 9.24e+00 chirality pdb=" P DC C 221 " pdb=" OP1 DC C 221 " pdb=" OP2 DC C 221 " pdb=" O5' DC C 221 " both_signs ideal model delta sigma weight residual True 2.35 -2.93 -0.59 2.00e-01 2.50e+01 8.60e+00 chirality pdb=" P DC H 48 " pdb=" OP1 DC H 48 " pdb=" OP2 DC H 48 " pdb=" O5' DC H 48 " both_signs ideal model delta sigma weight residual True 2.35 -2.93 -0.58 2.00e-01 2.50e+01 8.40e+00 ... (remaining 2364 not shown) Planarity restraints: 1540 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG I 42 " 0.036 5.00e-02 4.00e+02 5.41e-02 4.69e+00 pdb=" N PRO I 43 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO I 43 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO I 43 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DG C 202 " 0.001 2.00e-02 2.50e+03 1.17e-02 4.09e+00 pdb=" N9 DG C 202 " 0.008 2.00e-02 2.50e+03 pdb=" C8 DG C 202 " -0.001 2.00e-02 2.50e+03 pdb=" N7 DG C 202 " 0.000 2.00e-02 2.50e+03 pdb=" C5 DG C 202 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DG C 202 " -0.013 2.00e-02 2.50e+03 pdb=" O6 DG C 202 " 0.012 2.00e-02 2.50e+03 pdb=" N1 DG C 202 " 0.004 2.00e-02 2.50e+03 pdb=" C2 DG C 202 " -0.030 2.00e-02 2.50e+03 pdb=" N2 DG C 202 " 0.019 2.00e-02 2.50e+03 pdb=" N3 DG C 202 " 0.000 2.00e-02 2.50e+03 pdb=" C4 DG C 202 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE R 79 " -0.032 5.00e-02 4.00e+02 4.79e-02 3.68e+00 pdb=" N PRO R 80 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO R 80 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO R 80 " -0.027 5.00e-02 4.00e+02 ... (remaining 1537 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1301 2.74 - 3.28: 12529 3.28 - 3.82: 27024 3.82 - 4.36: 30349 4.36 - 4.90: 44242 Nonbonded interactions: 115445 Sorted by model distance: nonbonded pdb=" N2 DG C 262 " pdb=" O2 DC H 53 " model vdw 2.200 2.496 nonbonded pdb=" N2 DG C 181 " pdb=" O2 DC H 134 " model vdw 2.201 2.496 nonbonded pdb=" OG SER I 57 " pdb=" OE1 GLU I 59 " model vdw 2.209 3.040 nonbonded pdb=" OP2 DG C 187 " pdb=" OG SER S 53 " model vdw 2.225 3.040 nonbonded pdb=" O2 DC C 180 " pdb=" N2 DG H 135 " model vdw 2.227 2.496 ... (remaining 115440 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'I' selection = (chain 'O' and resid 38 through 135) } ncs_group { reference = (chain 'J' and ((resid 21 through 23 and (name N or name CA or name C or name O \ or name CB )) or resid 24 through 102)) selection = (chain 'Q' and resid 21 through 102) } ncs_group { reference = (chain 'K' and resid 12 through 119) selection = (chain 'R' and ((resid 12 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 56 or (resid 57 and (name N or name CA or name \ C or name O or name CB )) or resid 58 through 61 or (resid 62 and (name N or na \ me CA or name C or name O or name CB )) or resid 63 through 93 or (resid 94 and \ (name N or name CA or name C or name O or name CB )) or resid 95 through 119)) } ncs_group { reference = chain 'M' selection = (chain 'S' and (resid 28 through 105 or (resid 106 through 107 and (name N or na \ me CA or name C or name O or name CB )) or resid 108 through 122)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.23 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.520 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 43.610 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 14313 Z= 0.244 Angle : 0.710 9.048 20699 Z= 0.390 Chirality : 0.060 0.608 2367 Planarity : 0.004 0.054 1540 Dihedral : 30.149 179.048 6105 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 0.85 % Allowed : 30.31 % Favored : 68.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.28), residues: 879 helix: 1.55 (0.22), residues: 553 sheet: 1.21 (1.16), residues: 21 loop : -1.17 (0.33), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 176 HIS 0.004 0.001 HIS S 79 PHE 0.009 0.001 PHE J 100 TYR 0.020 0.002 TYR J 88 ARG 0.009 0.000 ARG J 95 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 138 time to evaluate : 0.988 Fit side-chains REVERT: I 59 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.7419 (pm20) REVERT: M 61 SER cc_start: 0.9096 (m) cc_final: 0.8864 (m) REVERT: Q 91 LYS cc_start: 0.8994 (ttpt) cc_final: 0.8785 (ttmm) outliers start: 6 outliers final: 2 residues processed: 140 average time/residue: 0.3374 time to fit residues: 62.9131 Evaluate side-chains 140 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 137 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 59 GLU Chi-restraints excluded: chain J residue 62 LEU Chi-restraints excluded: chain M residue 44 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 97 optimal weight: 2.9990 chunk 87 optimal weight: 0.5980 chunk 48 optimal weight: 3.9990 chunk 29 optimal weight: 8.9990 chunk 58 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 90 optimal weight: 4.9990 chunk 34 optimal weight: 5.9990 chunk 54 optimal weight: 0.9980 chunk 67 optimal weight: 6.9990 chunk 104 optimal weight: 0.5980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 84 GLN ** M 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 108 ASN Q 25 ASN Q 93 GLN ** R 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.1002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 14313 Z= 0.254 Angle : 0.632 8.701 20699 Z= 0.365 Chirality : 0.038 0.152 2367 Planarity : 0.004 0.052 1540 Dihedral : 32.558 179.151 4442 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 3.40 % Allowed : 28.33 % Favored : 68.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.28), residues: 879 helix: 1.75 (0.22), residues: 575 sheet: 0.58 (1.19), residues: 21 loop : -1.18 (0.34), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 176 HIS 0.004 0.001 HIS S 106 PHE 0.011 0.001 PHE J 100 TYR 0.021 0.002 TYR J 88 ARG 0.007 0.001 ARG J 95 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 161 time to evaluate : 0.943 Fit side-chains REVERT: J 78 ARG cc_start: 0.8907 (ptp90) cc_final: 0.8293 (ptt-90) REVERT: K 73 ASN cc_start: 0.8540 (t0) cc_final: 0.8325 (t0) REVERT: M 44 GLN cc_start: 0.8630 (tt0) cc_final: 0.8108 (tt0) REVERT: M 61 SER cc_start: 0.9121 (m) cc_final: 0.8878 (m) REVERT: O 73 GLU cc_start: 0.9102 (tm-30) cc_final: 0.8528 (tt0) REVERT: O 81 ASP cc_start: 0.7896 (t0) cc_final: 0.7636 (t0) REVERT: Q 91 LYS cc_start: 0.9068 (ttpt) cc_final: 0.8757 (ttmm) REVERT: R 89 ASN cc_start: 0.8644 (m-40) cc_final: 0.8014 (m-40) REVERT: S 37 TYR cc_start: 0.9256 (m-80) cc_final: 0.8996 (m-80) REVERT: S 118 TYR cc_start: 0.8374 (t80) cc_final: 0.8160 (t80) outliers start: 24 outliers final: 12 residues processed: 173 average time/residue: 0.3298 time to fit residues: 75.7918 Evaluate side-chains 155 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 143 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 70 LEU Chi-restraints excluded: chain J residue 43 VAL Chi-restraints excluded: chain J residue 50 ILE Chi-restraints excluded: chain J residue 84 MET Chi-restraints excluded: chain K residue 110 ASN Chi-restraints excluded: chain M residue 90 GLU Chi-restraints excluded: chain Q residue 82 THR Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain R residue 83 LEU Chi-restraints excluded: chain S residue 36 ILE Chi-restraints excluded: chain S residue 43 LYS Chi-restraints excluded: chain S residue 98 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 58 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 chunk 86 optimal weight: 0.2980 chunk 71 optimal weight: 4.9990 chunk 28 optimal weight: 10.0000 chunk 104 optimal weight: 3.9990 chunk 113 optimal weight: 0.5980 chunk 93 optimal weight: 0.9980 chunk 103 optimal weight: 0.5980 chunk 35 optimal weight: 6.9990 chunk 83 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 25 ASN ** R 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.1188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14313 Z= 0.212 Angle : 0.611 9.082 20699 Z= 0.353 Chirality : 0.037 0.174 2367 Planarity : 0.004 0.054 1540 Dihedral : 32.509 179.093 4434 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 3.26 % Allowed : 28.75 % Favored : 67.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.28), residues: 879 helix: 1.91 (0.22), residues: 575 sheet: 0.28 (1.20), residues: 21 loop : -1.13 (0.34), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 176 HIS 0.003 0.001 HIS J 75 PHE 0.007 0.001 PHE A 190 TYR 0.015 0.002 TYR Q 88 ARG 0.007 0.000 ARG J 95 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 152 time to evaluate : 1.019 Fit side-chains revert: symmetry clash REVERT: D 4 PHE cc_start: 0.6931 (OUTLIER) cc_final: 0.6715 (m-80) REVERT: K 25 PHE cc_start: 0.8909 (OUTLIER) cc_final: 0.7865 (t80) REVERT: M 44 GLN cc_start: 0.8661 (tt0) cc_final: 0.8140 (tt0) REVERT: M 61 SER cc_start: 0.9094 (m) cc_final: 0.8860 (m) REVERT: O 59 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.7857 (pm20) REVERT: O 73 GLU cc_start: 0.9106 (tm-30) cc_final: 0.8528 (tt0) REVERT: R 89 ASN cc_start: 0.8558 (m-40) cc_final: 0.7865 (m-40) outliers start: 23 outliers final: 9 residues processed: 166 average time/residue: 0.3310 time to fit residues: 73.3174 Evaluate side-chains 158 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 146 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 4 PHE Chi-restraints excluded: chain I residue 65 LEU Chi-restraints excluded: chain I residue 70 LEU Chi-restraints excluded: chain J residue 43 VAL Chi-restraints excluded: chain J residue 50 ILE Chi-restraints excluded: chain J residue 84 MET Chi-restraints excluded: chain K residue 25 PHE Chi-restraints excluded: chain K residue 110 ASN Chi-restraints excluded: chain O residue 59 GLU Chi-restraints excluded: chain R residue 20 ARG Chi-restraints excluded: chain S residue 36 ILE Chi-restraints excluded: chain S residue 98 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 chunk 11 optimal weight: 6.9990 chunk 49 optimal weight: 3.9990 chunk 70 optimal weight: 10.0000 chunk 104 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 chunk 99 optimal weight: 0.8980 chunk 29 optimal weight: 8.9990 chunk 92 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 2 GLN I 76 GLN I 125 GLN ** J 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 25 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.1610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 14313 Z= 0.270 Angle : 0.636 10.997 20699 Z= 0.365 Chirality : 0.038 0.196 2367 Planarity : 0.004 0.053 1540 Dihedral : 32.594 179.388 4434 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 4.96 % Allowed : 28.47 % Favored : 66.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.28), residues: 879 helix: 1.90 (0.22), residues: 578 sheet: 0.60 (1.16), residues: 21 loop : -1.14 (0.34), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 176 HIS 0.004 0.001 HIS R 82 PHE 0.008 0.001 PHE A 190 TYR 0.026 0.002 TYR Q 88 ARG 0.008 0.001 ARG J 95 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 150 time to evaluate : 1.106 Fit side-chains REVERT: D 6 LYS cc_start: 0.8214 (mmtm) cc_final: 0.6730 (tppt) REVERT: I 134 ARG cc_start: 0.7940 (OUTLIER) cc_final: 0.7731 (ttm-80) REVERT: K 25 PHE cc_start: 0.9006 (OUTLIER) cc_final: 0.7913 (t80) REVERT: K 73 ASN cc_start: 0.8558 (t0) cc_final: 0.8310 (t0) REVERT: O 51 ILE cc_start: 0.8628 (OUTLIER) cc_final: 0.8162 (mt) REVERT: O 56 LYS cc_start: 0.8288 (ttpt) cc_final: 0.7666 (ttpp) REVERT: O 59 GLU cc_start: 0.8518 (OUTLIER) cc_final: 0.7950 (pm20) REVERT: S 90 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7517 (mm-30) outliers start: 35 outliers final: 16 residues processed: 174 average time/residue: 0.3248 time to fit residues: 75.9773 Evaluate side-chains 165 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 144 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain I residue 65 LEU Chi-restraints excluded: chain I residue 70 LEU Chi-restraints excluded: chain I residue 134 ARG Chi-restraints excluded: chain J residue 43 VAL Chi-restraints excluded: chain J residue 50 ILE Chi-restraints excluded: chain J residue 84 MET Chi-restraints excluded: chain K residue 25 PHE Chi-restraints excluded: chain K residue 114 VAL Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain M residue 52 SER Chi-restraints excluded: chain O residue 51 ILE Chi-restraints excluded: chain O residue 59 GLU Chi-restraints excluded: chain O residue 65 LEU Chi-restraints excluded: chain R residue 20 ARG Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain R residue 83 LEU Chi-restraints excluded: chain S residue 36 ILE Chi-restraints excluded: chain S residue 84 SER Chi-restraints excluded: chain S residue 90 GLU Chi-restraints excluded: chain S residue 98 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 63 optimal weight: 3.9990 chunk 1 optimal weight: 7.9990 chunk 82 optimal weight: 0.6980 chunk 45 optimal weight: 0.9980 chunk 94 optimal weight: 0.6980 chunk 76 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 chunk 56 optimal weight: 0.8980 chunk 99 optimal weight: 0.3980 chunk 28 optimal weight: 10.0000 chunk 37 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 76 GLN ** J 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 25 ASN S 79 HIS S 81 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.1796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 14313 Z= 0.203 Angle : 0.607 10.656 20699 Z= 0.351 Chirality : 0.036 0.206 2367 Planarity : 0.004 0.059 1540 Dihedral : 32.434 179.939 4434 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 4.39 % Allowed : 27.34 % Favored : 68.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.29), residues: 879 helix: 2.09 (0.22), residues: 577 sheet: 0.44 (1.17), residues: 21 loop : -1.09 (0.34), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 176 HIS 0.005 0.001 HIS S 79 PHE 0.010 0.001 PHE J 100 TYR 0.012 0.002 TYR M 118 ARG 0.007 0.000 ARG J 95 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 160 time to evaluate : 1.035 Fit side-chains REVERT: D 1 MET cc_start: 0.6251 (mtt) cc_final: 0.5895 (mtt) REVERT: D 6 LYS cc_start: 0.8136 (mmtm) cc_final: 0.6850 (tppt) REVERT: K 25 PHE cc_start: 0.8935 (OUTLIER) cc_final: 0.7884 (t80) REVERT: K 73 ASN cc_start: 0.8597 (t0) cc_final: 0.8374 (t0) REVERT: M 44 GLN cc_start: 0.8551 (tt0) cc_final: 0.7985 (tt0) REVERT: M 98 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8341 (mm) REVERT: O 51 ILE cc_start: 0.8635 (OUTLIER) cc_final: 0.8220 (mt) REVERT: O 56 LYS cc_start: 0.8260 (ttpt) cc_final: 0.7636 (ttpp) REVERT: O 59 GLU cc_start: 0.8604 (OUTLIER) cc_final: 0.7996 (pm20) REVERT: O 74 ILE cc_start: 0.8964 (tt) cc_final: 0.8512 (mt) REVERT: O 81 ASP cc_start: 0.7949 (t0) cc_final: 0.7502 (t0) REVERT: R 89 ASN cc_start: 0.8404 (m-40) cc_final: 0.8109 (m-40) REVERT: S 31 LYS cc_start: 0.8038 (mmpt) cc_final: 0.7694 (mmpt) REVERT: S 43 LYS cc_start: 0.9021 (OUTLIER) cc_final: 0.8809 (tptt) outliers start: 31 outliers final: 17 residues processed: 183 average time/residue: 0.3321 time to fit residues: 81.1258 Evaluate side-chains 168 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 146 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain I residue 65 LEU Chi-restraints excluded: chain I residue 70 LEU Chi-restraints excluded: chain I residue 76 GLN Chi-restraints excluded: chain I residue 117 VAL Chi-restraints excluded: chain J residue 43 VAL Chi-restraints excluded: chain J residue 50 ILE Chi-restraints excluded: chain J residue 84 MET Chi-restraints excluded: chain K residue 25 PHE Chi-restraints excluded: chain K residue 85 LEU Chi-restraints excluded: chain K residue 114 VAL Chi-restraints excluded: chain M residue 98 LEU Chi-restraints excluded: chain O residue 51 ILE Chi-restraints excluded: chain O residue 59 GLU Chi-restraints excluded: chain O residue 65 LEU Chi-restraints excluded: chain R residue 19 SER Chi-restraints excluded: chain R residue 20 ARG Chi-restraints excluded: chain R residue 83 LEU Chi-restraints excluded: chain S residue 36 ILE Chi-restraints excluded: chain S residue 43 LYS Chi-restraints excluded: chain S residue 84 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 100 optimal weight: 3.9990 chunk 21 optimal weight: 10.0000 chunk 65 optimal weight: 9.9990 chunk 27 optimal weight: 20.0000 chunk 111 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 9 optimal weight: 6.9990 chunk 36 optimal weight: 5.9990 chunk 58 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 76 GLN I 125 GLN ** M 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 79 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 14313 Z= 0.356 Angle : 0.674 10.861 20699 Z= 0.383 Chirality : 0.040 0.210 2367 Planarity : 0.005 0.053 1540 Dihedral : 32.665 177.575 4434 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 5.38 % Allowed : 27.62 % Favored : 67.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.28), residues: 879 helix: 1.77 (0.22), residues: 578 sheet: 0.38 (1.04), residues: 21 loop : -1.17 (0.34), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 176 HIS 0.006 0.002 HIS S 106 PHE 0.009 0.002 PHE I 67 TYR 0.034 0.002 TYR J 88 ARG 0.007 0.001 ARG J 95 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 148 time to evaluate : 0.958 Fit side-chains REVERT: I 134 ARG cc_start: 0.7818 (OUTLIER) cc_final: 0.7556 (ttm-80) REVERT: K 25 PHE cc_start: 0.9060 (OUTLIER) cc_final: 0.7847 (t80) REVERT: K 42 ARG cc_start: 0.7869 (OUTLIER) cc_final: 0.7079 (ptm160) REVERT: K 73 ASN cc_start: 0.8617 (t0) cc_final: 0.8396 (t0) REVERT: M 98 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8323 (mm) REVERT: O 51 ILE cc_start: 0.8640 (OUTLIER) cc_final: 0.8151 (mt) REVERT: O 59 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.7962 (pm20) REVERT: O 81 ASP cc_start: 0.8106 (t0) cc_final: 0.7641 (t0) REVERT: Q 91 LYS cc_start: 0.9095 (ttmm) cc_final: 0.8854 (ttmm) REVERT: R 76 THR cc_start: 0.9142 (p) cc_final: 0.8898 (t) REVERT: S 90 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.7652 (mm-30) outliers start: 38 outliers final: 14 residues processed: 175 average time/residue: 0.3327 time to fit residues: 77.6060 Evaluate side-chains 162 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 141 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 65 LEU Chi-restraints excluded: chain I residue 70 LEU Chi-restraints excluded: chain I residue 71 VAL Chi-restraints excluded: chain I residue 117 VAL Chi-restraints excluded: chain I residue 134 ARG Chi-restraints excluded: chain J residue 50 ILE Chi-restraints excluded: chain J residue 84 MET Chi-restraints excluded: chain K residue 25 PHE Chi-restraints excluded: chain K residue 42 ARG Chi-restraints excluded: chain K residue 110 ASN Chi-restraints excluded: chain K residue 114 VAL Chi-restraints excluded: chain M residue 52 SER Chi-restraints excluded: chain M residue 98 LEU Chi-restraints excluded: chain O residue 51 ILE Chi-restraints excluded: chain O residue 59 GLU Chi-restraints excluded: chain O residue 65 LEU Chi-restraints excluded: chain R residue 19 SER Chi-restraints excluded: chain R residue 83 LEU Chi-restraints excluded: chain S residue 36 ILE Chi-restraints excluded: chain S residue 84 SER Chi-restraints excluded: chain S residue 90 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 12 optimal weight: 6.9990 chunk 63 optimal weight: 1.9990 chunk 81 optimal weight: 0.3980 chunk 62 optimal weight: 0.0970 chunk 93 optimal weight: 0.7980 chunk 110 optimal weight: 0.7980 chunk 69 optimal weight: 2.9990 chunk 67 optimal weight: 4.9990 chunk 51 optimal weight: 7.9990 chunk 68 optimal weight: 0.8980 chunk 44 optimal weight: 0.6980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 76 GLN I 125 GLN M 46 HIS ** M 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.2125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 14313 Z= 0.197 Angle : 0.611 10.490 20699 Z= 0.351 Chirality : 0.037 0.206 2367 Planarity : 0.004 0.058 1540 Dihedral : 32.437 178.784 4434 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 3.68 % Allowed : 28.90 % Favored : 67.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.29), residues: 879 helix: 2.05 (0.22), residues: 579 sheet: 1.00 (1.16), residues: 21 loop : -1.10 (0.34), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 176 HIS 0.005 0.001 HIS M 46 PHE 0.011 0.001 PHE J 100 TYR 0.013 0.001 TYR J 88 ARG 0.006 0.000 ARG Q 95 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 155 time to evaluate : 1.043 Fit side-chains REVERT: D 6 LYS cc_start: 0.7690 (mmtm) cc_final: 0.6126 (tppt) REVERT: D 67 LEU cc_start: 0.7914 (mm) cc_final: 0.7415 (mm) REVERT: K 25 PHE cc_start: 0.8936 (OUTLIER) cc_final: 0.7810 (t80) REVERT: M 44 GLN cc_start: 0.8756 (tt0) cc_final: 0.7900 (tt0) REVERT: M 98 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8316 (mm) REVERT: O 51 ILE cc_start: 0.8640 (OUTLIER) cc_final: 0.8193 (mt) REVERT: O 59 GLU cc_start: 0.8655 (OUTLIER) cc_final: 0.8092 (pm20) REVERT: O 81 ASP cc_start: 0.8018 (t0) cc_final: 0.7575 (t0) REVERT: Q 27 GLN cc_start: 0.9272 (mm110) cc_final: 0.8999 (mm-40) REVERT: Q 84 MET cc_start: 0.8705 (mmm) cc_final: 0.8433 (mmp) REVERT: S 43 LYS cc_start: 0.9023 (OUTLIER) cc_final: 0.8803 (tptt) outliers start: 26 outliers final: 17 residues processed: 173 average time/residue: 0.3137 time to fit residues: 73.6719 Evaluate side-chains 170 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 148 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 TRP Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain I residue 65 LEU Chi-restraints excluded: chain I residue 70 LEU Chi-restraints excluded: chain I residue 115 LYS Chi-restraints excluded: chain I residue 117 VAL Chi-restraints excluded: chain J residue 43 VAL Chi-restraints excluded: chain J residue 50 ILE Chi-restraints excluded: chain J residue 84 MET Chi-restraints excluded: chain K residue 25 PHE Chi-restraints excluded: chain K residue 114 VAL Chi-restraints excluded: chain M residue 98 LEU Chi-restraints excluded: chain M residue 103 LEU Chi-restraints excluded: chain O residue 51 ILE Chi-restraints excluded: chain O residue 59 GLU Chi-restraints excluded: chain O residue 65 LEU Chi-restraints excluded: chain O residue 87 SER Chi-restraints excluded: chain R residue 19 SER Chi-restraints excluded: chain R residue 83 LEU Chi-restraints excluded: chain S residue 36 ILE Chi-restraints excluded: chain S residue 43 LYS Chi-restraints excluded: chain S residue 84 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 0.0570 chunk 33 optimal weight: 5.9990 chunk 21 optimal weight: 9.9990 chunk 70 optimal weight: 10.0000 chunk 75 optimal weight: 3.9990 chunk 54 optimal weight: 0.5980 chunk 10 optimal weight: 5.9990 chunk 87 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 106 optimal weight: 10.0000 chunk 96 optimal weight: 5.9990 overall best weight: 1.9304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 76 GLN I 125 GLN M 46 HIS ** M 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 14313 Z= 0.292 Angle : 0.641 9.670 20699 Z= 0.367 Chirality : 0.039 0.218 2367 Planarity : 0.004 0.055 1540 Dihedral : 32.568 177.395 4434 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 4.25 % Allowed : 29.18 % Favored : 66.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.28), residues: 879 helix: 1.90 (0.22), residues: 579 sheet: 0.42 (1.15), residues: 21 loop : -1.17 (0.34), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 176 HIS 0.004 0.001 HIS S 106 PHE 0.008 0.001 PHE A 190 TYR 0.025 0.002 TYR J 88 ARG 0.008 0.001 ARG I 131 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 143 time to evaluate : 1.050 Fit side-chains REVERT: I 134 ARG cc_start: 0.7830 (OUTLIER) cc_final: 0.7592 (ttm-80) REVERT: K 25 PHE cc_start: 0.9023 (OUTLIER) cc_final: 0.7817 (t80) REVERT: K 42 ARG cc_start: 0.7816 (OUTLIER) cc_final: 0.7055 (ptm160) REVERT: K 74 LYS cc_start: 0.8889 (ptpp) cc_final: 0.8532 (ttpt) REVERT: M 98 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8308 (mm) REVERT: O 51 ILE cc_start: 0.8639 (OUTLIER) cc_final: 0.8168 (mt) REVERT: O 59 GLU cc_start: 0.8585 (OUTLIER) cc_final: 0.8017 (pm20) REVERT: O 73 GLU cc_start: 0.9148 (tm-30) cc_final: 0.8806 (tt0) REVERT: O 81 ASP cc_start: 0.8065 (t0) cc_final: 0.7609 (t0) REVERT: Q 97 LEU cc_start: 0.9308 (OUTLIER) cc_final: 0.8841 (tp) REVERT: R 76 THR cc_start: 0.9151 (p) cc_final: 0.8939 (t) outliers start: 30 outliers final: 16 residues processed: 165 average time/residue: 0.3364 time to fit residues: 74.3841 Evaluate side-chains 158 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 135 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 TRP Chi-restraints excluded: chain I residue 65 LEU Chi-restraints excluded: chain I residue 70 LEU Chi-restraints excluded: chain I residue 71 VAL Chi-restraints excluded: chain I residue 118 THR Chi-restraints excluded: chain I residue 134 ARG Chi-restraints excluded: chain J residue 43 VAL Chi-restraints excluded: chain J residue 50 ILE Chi-restraints excluded: chain J residue 84 MET Chi-restraints excluded: chain K residue 25 PHE Chi-restraints excluded: chain K residue 42 ARG Chi-restraints excluded: chain K residue 85 LEU Chi-restraints excluded: chain K residue 110 ASN Chi-restraints excluded: chain K residue 114 VAL Chi-restraints excluded: chain M residue 98 LEU Chi-restraints excluded: chain M residue 103 LEU Chi-restraints excluded: chain O residue 51 ILE Chi-restraints excluded: chain O residue 59 GLU Chi-restraints excluded: chain O residue 65 LEU Chi-restraints excluded: chain Q residue 97 LEU Chi-restraints excluded: chain R residue 83 LEU Chi-restraints excluded: chain S residue 36 ILE Chi-restraints excluded: chain S residue 84 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 2.9990 chunk 106 optimal weight: 0.8980 chunk 62 optimal weight: 0.3980 chunk 44 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 31 optimal weight: 7.9990 chunk 93 optimal weight: 0.7980 chunk 97 optimal weight: 0.4980 chunk 102 optimal weight: 2.9990 chunk 67 optimal weight: 0.0970 chunk 109 optimal weight: 0.9980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 76 GLN M 46 HIS ** M 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.2437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 14313 Z= 0.189 Angle : 0.604 8.877 20699 Z= 0.349 Chirality : 0.036 0.237 2367 Planarity : 0.004 0.059 1540 Dihedral : 32.401 178.576 4434 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 3.54 % Allowed : 29.32 % Favored : 67.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (0.29), residues: 879 helix: 2.17 (0.22), residues: 574 sheet: 0.13 (1.13), residues: 22 loop : -0.89 (0.35), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 176 HIS 0.004 0.001 HIS J 75 PHE 0.012 0.001 PHE A 190 TYR 0.013 0.001 TYR K 39 ARG 0.008 0.000 ARG Q 95 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 151 time to evaluate : 1.026 Fit side-chains REVERT: D 6 LYS cc_start: 0.7531 (mmtm) cc_final: 0.6279 (tppt) REVERT: D 67 LEU cc_start: 0.7961 (mm) cc_final: 0.7366 (mm) REVERT: K 25 PHE cc_start: 0.8854 (OUTLIER) cc_final: 0.7749 (t80) REVERT: K 35 ARG cc_start: 0.8072 (mtm110) cc_final: 0.7774 (mtp-110) REVERT: K 56 GLU cc_start: 0.8213 (tt0) cc_final: 0.8003 (tt0) REVERT: K 74 LYS cc_start: 0.8848 (ptpp) cc_final: 0.8530 (ttpt) REVERT: M 44 GLN cc_start: 0.8699 (tt0) cc_final: 0.7864 (tt0) REVERT: M 98 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8371 (mt) REVERT: O 51 ILE cc_start: 0.8607 (OUTLIER) cc_final: 0.8143 (mt) REVERT: O 59 GLU cc_start: 0.8653 (OUTLIER) cc_final: 0.8121 (pm20) REVERT: O 73 GLU cc_start: 0.9130 (tm-30) cc_final: 0.8894 (tt0) REVERT: O 81 ASP cc_start: 0.7958 (t0) cc_final: 0.7537 (t0) REVERT: Q 97 LEU cc_start: 0.9218 (OUTLIER) cc_final: 0.8789 (tp) REVERT: S 43 LYS cc_start: 0.8996 (OUTLIER) cc_final: 0.8778 (tptt) outliers start: 25 outliers final: 15 residues processed: 169 average time/residue: 0.3181 time to fit residues: 72.5265 Evaluate side-chains 163 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 142 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 TRP Chi-restraints excluded: chain I residue 65 LEU Chi-restraints excluded: chain I residue 70 LEU Chi-restraints excluded: chain I residue 71 VAL Chi-restraints excluded: chain I residue 107 THR Chi-restraints excluded: chain J residue 50 ILE Chi-restraints excluded: chain J residue 84 MET Chi-restraints excluded: chain K residue 25 PHE Chi-restraints excluded: chain K residue 114 VAL Chi-restraints excluded: chain M residue 98 LEU Chi-restraints excluded: chain O residue 51 ILE Chi-restraints excluded: chain O residue 59 GLU Chi-restraints excluded: chain O residue 65 LEU Chi-restraints excluded: chain Q residue 97 LEU Chi-restraints excluded: chain R residue 19 SER Chi-restraints excluded: chain R residue 20 ARG Chi-restraints excluded: chain R residue 83 LEU Chi-restraints excluded: chain S residue 36 ILE Chi-restraints excluded: chain S residue 43 LYS Chi-restraints excluded: chain S residue 84 SER Chi-restraints excluded: chain S residue 98 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 1.9990 chunk 51 optimal weight: 7.9990 chunk 75 optimal weight: 0.5980 chunk 114 optimal weight: 6.9990 chunk 105 optimal weight: 0.8980 chunk 91 optimal weight: 0.7980 chunk 9 optimal weight: 6.9990 chunk 70 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 97 optimal weight: 0.3980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 76 GLN M 46 HIS ** M 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.2467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 14313 Z= 0.199 Angle : 0.606 8.626 20699 Z= 0.349 Chirality : 0.037 0.227 2367 Planarity : 0.004 0.059 1540 Dihedral : 32.412 177.966 4434 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 3.40 % Allowed : 29.04 % Favored : 67.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.29), residues: 879 helix: 2.21 (0.22), residues: 574 sheet: -0.19 (1.14), residues: 22 loop : -0.88 (0.36), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 176 HIS 0.004 0.001 HIS J 75 PHE 0.009 0.001 PHE J 100 TYR 0.017 0.001 TYR K 39 ARG 0.008 0.000 ARG Q 95 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 145 time to evaluate : 1.078 Fit side-chains REVERT: D 3 ILE cc_start: 0.4979 (mm) cc_final: 0.3989 (mm) REVERT: D 6 LYS cc_start: 0.7734 (mmtm) cc_final: 0.6216 (tppt) REVERT: D 67 LEU cc_start: 0.7941 (mm) cc_final: 0.7355 (mm) REVERT: K 25 PHE cc_start: 0.8889 (OUTLIER) cc_final: 0.7757 (t80) REVERT: K 56 GLU cc_start: 0.8219 (tt0) cc_final: 0.8018 (tt0) REVERT: K 74 LYS cc_start: 0.8829 (ptpp) cc_final: 0.8536 (ttpt) REVERT: M 44 GLN cc_start: 0.8676 (tt0) cc_final: 0.7834 (tt0) REVERT: M 98 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8339 (mm) REVERT: O 51 ILE cc_start: 0.8637 (OUTLIER) cc_final: 0.8214 (mt) REVERT: O 59 GLU cc_start: 0.8617 (OUTLIER) cc_final: 0.8089 (pm20) REVERT: O 73 GLU cc_start: 0.9110 (tm-30) cc_final: 0.8890 (tt0) REVERT: O 81 ASP cc_start: 0.7971 (t0) cc_final: 0.7541 (t0) REVERT: Q 97 LEU cc_start: 0.9255 (OUTLIER) cc_final: 0.8774 (tp) outliers start: 24 outliers final: 16 residues processed: 163 average time/residue: 0.3239 time to fit residues: 71.2616 Evaluate side-chains 162 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 141 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 TRP Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain I residue 65 LEU Chi-restraints excluded: chain I residue 70 LEU Chi-restraints excluded: chain I residue 71 VAL Chi-restraints excluded: chain I residue 107 THR Chi-restraints excluded: chain J residue 43 VAL Chi-restraints excluded: chain J residue 50 ILE Chi-restraints excluded: chain J residue 84 MET Chi-restraints excluded: chain K residue 25 PHE Chi-restraints excluded: chain K residue 114 VAL Chi-restraints excluded: chain M residue 98 LEU Chi-restraints excluded: chain O residue 51 ILE Chi-restraints excluded: chain O residue 59 GLU Chi-restraints excluded: chain O residue 65 LEU Chi-restraints excluded: chain Q residue 97 LEU Chi-restraints excluded: chain R residue 20 ARG Chi-restraints excluded: chain R residue 83 LEU Chi-restraints excluded: chain S residue 36 ILE Chi-restraints excluded: chain S residue 84 SER Chi-restraints excluded: chain S residue 98 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 27 optimal weight: 20.0000 chunk 84 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 chunk 25 optimal weight: 30.0000 chunk 91 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 93 optimal weight: 1.9990 chunk 11 optimal weight: 6.9990 chunk 16 optimal weight: 6.9990 chunk 80 optimal weight: 0.9990 chunk 5 optimal weight: 6.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 76 GLN I 125 GLN M 46 HIS ** M 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 75 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.171488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.111756 restraints weight = 39040.204| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 2.50 r_work: 0.2962 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2957 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2957 r_free = 0.2957 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2957 r_free = 0.2957 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2957 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 14313 Z= 0.400 Angle : 0.694 9.933 20699 Z= 0.393 Chirality : 0.042 0.223 2367 Planarity : 0.005 0.052 1540 Dihedral : 32.672 175.651 4434 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 3.68 % Allowed : 29.04 % Favored : 67.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.28), residues: 879 helix: 1.74 (0.22), residues: 579 sheet: -0.18 (1.17), residues: 22 loop : -1.17 (0.35), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 176 HIS 0.007 0.002 HIS S 106 PHE 0.008 0.002 PHE S 62 TYR 0.035 0.003 TYR J 88 ARG 0.008 0.001 ARG Q 95 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2636.60 seconds wall clock time: 47 minutes 27.58 seconds (2847.58 seconds total)